Thomas Zeiser

Some comments by Thomas Zeiser about HPC@RRZE and other things


What are potential applications to exploit the GlobusToolkit / Unicore installation at RRZE?

What are potential applications to exploit the GlobusToolkit / Unicore installation at RRZE?

Although there are still some difficulties in getting the GlobusToolkit installation running, I’m wodering who will use it.

The GlobusToolkit is basically just a framework. Therefore, users probably have to spend some effort to make their applications GT4-aware … Just using GSIftp or SGIssh probably is not a big progress …

With Unicore, the situation might be slightly better as there is a nice GUI. However, also this GUI has to be extended by plugins written in Java to realy make progress. Just using the shell plugin does not really help. But at least, the Unicore client can easily be installed on the user’s system without requiering as host certificate or installing many hunderds MB as it is the case for GT4.

But anyway, my (current) feeling is that all grid services will have the same future as advanced debugger: ssh/slogin/scp will remain the tool of choise as printf will remain the most popular "debugger". But I’d be gladed to be convinced otherwise (by practial examples).

SGI Altix extension

Recently, the SGI Altix at RRZE has been extended. We now have a batch-only system altix-batch (an SGI Altix 3700 with 32 CPUs and 128 GB shared memory) and a front-end system altix (an SGI Altix 330 with 16 CPUs and 32 GB shared memory; 4 CPUs + 8 GB are used as login partition (boot cpuset) – the remaining ones are also used for batch processing).

An important thing to note is that the new machine has only half the amount of memory per CPU as the "old" one. As the cpusets introduced with SuSE SLES9/SGI ProPack4.x do not have all the features known from the old SGI Origin cpusets, in particular policy kill is missing, the systems starts swapping as soon as one process exceeds the amount of memory available in its cpuset. As a results, the complete system becomes un-responsive.

Therefore, it is very important to request the correct machine or to specify the amount of memory required in addition to the number of CPUs. Also the amount of interactive work is now much more limitated as we now have a login partition (boot cpuset) which only have access to 4 CPUs and 8 GB of memory!

Check the official web page of the SGI Altic Systems at RRZE for more details and the correct syntax for specifying recource requirements.

Handling BibTeX files

BibTeX is the bibliography format if you are working with LaTeX. Emacs has a very nice mode for editing BibTeX files, in particular if you add

(setq bibtex-maintain-sorted-entries 1)
(setq bibtex-clean-entry-zap-empty-opts nil)

to your .emacs file. However, sometimes it can be easier to have a specialized GUI. People suggested

Both tools are said to be easy to use and to have many options for importing (e.g. directly from electronic data bases such as INSPEC) or exporting (e.g. to endnote). However, I never had time to test them …

STAR-CD 4.0 available

Since resently, STAR-CD 4.0 is available for x86 and x86_64. Unfortunately, the currently builds again require the ABSOFT compiler to include user subroutines 🙂 Further builds and support or IA64 and MS Windows hopefully apprear in the following months …

STAR-CD 4.0 has already installed on Cluster32. All STAR-CD users are encouraged to test this new version. Iy you are using user subroutines, some changes are probably required as CD-adapco moved from Fortran77 to Fortran90 and eliminated one common data structure. Check the documentation for more details.

For those, running STAR-CD on their local systems, the installation files are available at the usual place.